Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00809.N3

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 3318
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31


Found at i:262 original size:26 final size:26

Alignment explanation


    Indices: 226--387  Score: 288
    Period size: 26  Copynumber: 6.2  Consensus size: 26

        216 TGATACAAAT

                                   *  
        226 TGATAATAGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                                      
        252 TGATAATAGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                                      
        278 TGATAATAGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                                      
        304 TGATAATAGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                   *                  
        330 TGATAATGGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                   *               *  
        356 TGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                  
        382 TGATAA
          1 TGATAA

        388 GAATTTCATG


Statistics
Matches: 133,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  26  133  1.00

ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36


Consensus pattern (26 bp):   
TGATAATAGGTTAGGTAAATGTTCCA

Found at i:1124 original size:27 final size:27

Alignment explanation


    Indices: 1086--1208  Score: 147
    Period size: 27  Copynumber: 4.5  Consensus size: 27

       1076 AAGCGTTCTG

                  *            *       
       1086 GTGGCTATGCCACAAATATATGATCTA
          1 GTGGCTCTGCCACAAATATCTGATCTA

                                      *
       1113 GTGGCTCTGCCACAAATATCTGATCTG
          1 GTGGCTCTGCCACAAATATCTGATCTA

                          *       *   *
       1140 GTGGCTCTGCCACATATATCTGTTCTG
          1 GTGGCTCTGCCACAAATATCTGATCTA

                         * *            
       1167 GTGGCTCTGCCACGATTATCTGTATCTA
          1 GTGGCTCTGCCACAAATATCTG-ATCTA

               *     *    
       1195 GTGACTCTGTCACA
          1 GTGGCTCTGCCACA

       1209 TTATCTGTTC


Statistics
Matches: 82,  Mismatches: 13, Indels: 1
        0.85            0.14        0.01

Matches are distributed among these distances:
  27   68  0.83
  28   14  0.17

ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33


Consensus pattern (27 bp):   
GTGGCTCTGCCACAAATATCTGATCTA

Found at i:1171 original size:54 final size:55

Alignment explanation


    Indices: 1082--1221  Score: 176
    Period size: 54  Copynumber: 2.6  Consensus size: 55

       1072 GAGGAAGCGT

                      *       *    *  *   *                        
       1082 TCTGGTGGCTATGCCACAAATATATGATCTAGTGGCTCTGCCACAAATATCTG-A
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

                                                        * *        
       1136 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

               *   *     *                  
       1191 TCTAGTGACTCTGTCACAT-TATCTGTTCTGG
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG

       1222 CAGCCATGCT


Statistics
Matches: 75,  Mismatches: 10, Indels: 2
        0.86            0.11        0.02

Matches are distributed among these distances:
  54   58  0.77
  55   17  0.23

ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35


Consensus pattern (55 bp):   
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

Found at i:1981 original size:27 final size:26

Alignment explanation


    Indices: 1932--2044  Score: 118
    Period size: 27  Copynumber: 4.2  Consensus size: 26

       1922 GAGGAAGCGT

                  *   *        *       
       1932 TCTGGTAGCTATGCCACAAATATCTGA
          1 TCTGGTGGCTCTGCCAC-ATTATCTGA

               *                      *
       1959 TCTAGTGGCTCTGCCACATATATCTGT
          1 TCTGGTGGCTCTGCCACAT-TATCTGA

                                        
       1986 TCTGGTGGCTCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCAC-ATTATCTG-A

                   *     *           *
       2014 TCTGGTGACTCTGTCACATTATCTGT
          1 TCTGGTGGCTCTGCCACATTATCTGA

                 
       2040 TCTGG
          1 TCTGG

       2045 CAGCCATGCT


Statistics
Matches: 73,  Mismatches: 10, Indels: 7
        0.81            0.11        0.08

Matches are distributed among these distances:
  26    6  0.08
  27   50  0.68
  28   17  0.23

ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36


Consensus pattern (26 bp):   
TCTGGTGGCTCTGCCACATTATCTGA

Found at i:2037 original size:54 final size:54

Alignment explanation


    Indices: 1930--2053  Score: 151
    Period size: 54  Copynumber: 2.3  Consensus size: 54

       1920 TGGAGGAAGC

                                                *                 
       1930 GTTCTGGTAGCTATGCCACAAATATCTGATCTAGTGGCTCTGCCACATATATCT
          1 GTTCTGGTAGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCT

                    *   *      * *           *         *           
       1984 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
          1 GTTCTGGTAGCTATGCCACAAATATCTG-ATCTAGTGACTCTGCCACATATATCT

                   *   *    
       2038 GTTCTGGCAGCCATGC
          1 GTTCTGGTAGCTATGC

       2054 TGCAAATTCT


Statistics
Matches: 58,  Mismatches: 11, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  54   41  0.71
  55   17  0.29

ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35


Consensus pattern (54 bp):   
GTTCTGGTAGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCT
Done.